Risk factors for infection with influenza A(H3N2) virus on a US university campus, October–November 2021

Abstract Background Knowledge of the specific dynamics of influenza introduction and spread in university settings is limited. Methods Persons with acute respiratory illness symptoms received influenza testing by molecular assay during October 6–November 23, 2022. Viral sequencing and phylogenetic analysis were conducted on nasal swab samples from case‐patients. Case–control analysis of a voluntary survey of persons tested was used to identify factors associated with influenza; logistic regression was conducted to calculate odds ratios and 95% CIs. A subset of case‐patients tested during the first month of the outbreak was interviewed to identify sources of introduction and early spread. Results Among 3268 persons tested, 788 (24.1%) tested positive for influenza; 744 (22.8%) were included in the survey analysis. All 380 sequenced specimens were influenza A (H3N2) virus clade 3C.2a1b.2a.2, suggesting rapid transmission. Influenza (OR [95% CI]) was associated with indoor congregate dining (1.43 [1.002–2.03]), attending large gatherings indoors (1.83 [1.26–2.66]) or outdoors (2.33 [1.64–3.31]), and varied by residence type (apartment with ≥1 roommate: 2.93 [1.21–7.11], residence hall room alone: 4.18 [1.31–13.31], or with roommate: 6.09 [2.46–15.06], or fraternity/sorority house: 15.13 [4.30–53.21], all compared with single‐dwelling apartment). Odds of influenza were lower among persons who left campus for ≥1 day during the week before their influenza test (0.49 [0.32–0.75]). Almost all early cases reported attending large events. Conclusions Congregate living and activity settings on university campuses can lead to rapid spread of influenza following introduction. Isolating following a positive influenza test or administering antiviral medications to exposed persons may help mitigate outbreaks.


| INTRODUCTION
As congregate settings with dense residential facilities and sustained social interactions, university campuses are common sites for outbreaks of influenza and influenza-like illness (ILI). 1,2 In addition, campuses have high concentrations of young adults, who may be less likely to adopt behaviors that prevent or mitigate the spread of respiratory illness compared with other age groups. 1,[3][4][5] Although both viral characteristics 6,7 and demographic characteristics 8 may contribute to the likelihood of influenza, the social and environmental characteristics affecting the introduction and spread of influenza on university campuses are less understood.
Beginning in October 2021, a rapid increase in influenza A(H3N2) cases was reported by the University Health Service (UHS) at the University of Michigan in Ann Arbor, Michigan, USA, a university with more than 40 000 students, including approximately 11 000 who reside on campus. The unexpected outbreak represented some of the first substantial influenza activity reported during the COVID-19 pandemic and followed a surge in COVID-19 activity in Michigan. 9 To characterize the influenza outbreak, CDC staff arrived on November 15, 2021, to further investigate risk factors associated with influenza infection, in collaboration with the university, Michigan Department of Health and Human Services, and local partners. 6 Using a sample of students, staff, and university affiliates (e.g., visiting researchers and other employees) who received regular clinical testing for influenza during the outbreak, we retrospectively conducted viral sequencing and phylogenetic analysis of influenza-positive specimens to assess virus evolution during the outbreak, an online survey to assess factors associated with influenza, and more detailed interviews with a subset of early case-patients to better understand their exposures and the emergence of rapid transmission on campus.

| Study site and testing
University students, staff, and affiliates with symptoms of acute respiratory illness (ARI), including fever or chills, cough, shortness of breath or difficulty breathing, fatigue, muscle or body aches, headache, recent loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, or diarrhea, were eligible to schedule an appointment for testing at the University Health Service (UHS), a clinic located centrally on campus. UHS staff collected a nasal swab among persons presenting for testing. Swabs were tested by a quad rapid multiplex molecular assay for influenza A, influenza B, SARS-CoV-2, and respiratory syncytial virus (RSV) at the University of Michigan. 2 Cases were defined as persons receiving a positive test for influenza A at UHS during October 6-November 23, 2021 (no influenza B was detected); controls were defined as all persons testing negative for influenza during the same period, including those testing positive for SARS-CoV-2 or RSV. Among persons who received testing more than once during October 6-November 23, 2021, the first influenza Apositive test result was used, or if the person never received an influenza A-positive result, the first negative test result was used.

| Viral sequencing and phylogenetic analysis
RNA was extracted from nasal swab samples (cycle threshold: ≤30) using the MagMAX viral pathogen nucleic acid isolation kit on a Kingfisher instrument. The influenza A virus genome was amplified by reverse transcription polymerase chain reaction (RT-PCR) using universal influenza A primers 10 and SuperScript IV master mix (Thermofisher). NEBNext companion kits were used for Nanopore library preparation. Samples were pooled (up to 96 samples per pool) and sequenced on an Oxford Nanopore GridION. For each sample, a consensus sequence was created using IRMA iterative refinement meta-assembler. All samples were aligned to A/Darwin/9/2021 (clade 2a.2) using MAFFT. 11 A phylogenetic tree was constructed using IQ-TREE with a GTR substitution model, and a time tree was constructed using TreeTime. Molecular clock outliers were removed, and a revised time tree was constructed along with an estimate for the time to the most recent common ancestor. All data are currently available at the GISAID initiative (https://gisaid.org).

| Survey and interview analysis
All persons tested during October 6-November 23, 2021, received an email prompt and a link to a survey with a combination of multiple-choice and short-answer questions asking about their demographic characteristics, residential information, symptoms during their illness, and other risk factors (e.g., travel and event attendance) potentially associated with influenza infection. A casecontrol approach was used to identify factors associated with infection. Logistic regression was used to calculate odds ratios (95% CIs) of factors potentially associated with influenza infection. Odds ratios with 95% CIs that did not span 1.0 were considered statistically significant and are denoted in tables by bold font. Qualitative telephone interviews were conducted with a convenience sample of 21 case-patients who tested positive for influenza during October 6-November 2, 2021, the earliest phase of the outbreak (these case-patients did not necessarily also respond to the survey).   All analyses were performed using SAS 9.4 (Cary, NC). All activities (i.e., testing, sequencing, surveys, and interviews) were determined to be non-research public health surveillance by CDC and conducted consistent with applicable federal law and CDC policy   Several behaviors during the week prior to testing were also associated with influenza, as reported in the voluntary survey (Table 3).
Off-campus activities were associated with lower odds of influenza. indoor and outdoor activities were similarly associated with increased odds of infection, suggesting that large outdoor activities (e.g., football games) as well as indoor ones may have been important sites of transmission, although these categories were not mutually exclusive, and many respondents may have engaged in both. Recent work on COVID-19 has suggested that psychosocial characteristics typical of young adults, such as increased risk-taking, social experience-seeking, and less premeditation of consequences, 3,14 could have contributed to attending events or not masking during events or indoor interactions despite COVID-19 recommendations.
Early case-patients typically reported an interval of 2-3 days between presumed exposure and symptom onset, similar to that observed in previous influenza household transmission studies 15

| CONCLUSIONS
Investigation of influenza outbreaks on university campuses can help identify risk factors for transmission, as well as the social and residential dynamics that can amplify odds of being infected. Risk factors for influenza inflection, including exposure to persons who are ill, and living in congregate settings, are similar to those for COVID-19. In addition, introductions from one or two events can lead to rapid spread.
Interventions, such as encouraging vaccination, testing, and quarantining following a positive influenza test, or use of preventive antiviral medication following exposure, could be helpful in mitigating outbreaks in environments such as college campuses.

DATA AVAILABILITY STATEMENT
The data that support the findings of this study are available from the corresponding author upon reasonable request. The data are not publicly available due to privacy or ethical restrictions.